This is an result for the gene singatures as well as assigned cell type for each cluster based on Danaher et al.
knitr::opts_chunk$set(cache=TRUE)
sig_plot <- visualize_clusters(cluster_tsne$cell_type,cluster_tsne[c("TSNE.1","TSNE.2")],title="Danaher cell-type labels",legend_anno= sort(unique(cluster_tsne[,"name_type"])))+scale_color_manual(values = colorRampPalette(c("blue", "red","yellow"))( length(sort(unique(cluster_tsne[,"name_type"])))))+ annotate("text", x = tsne_center[, 1], y = tsne_center[, 2], size = 5,label=c(1:length(tsne_center[,1])))
sig_plot

top_sig <- data.frame(t(sapply(unique(all_type_expr_table$Cluster),function(x){ all_type_expr_table[all_type_expr_table$Cluster == x,][which(all_type_expr_table$precent_count[all_type_expr_table$Cluster == x] == max(all_type_expr_table$precent_count[all_type_expr_table$Cluster == x])),] })))
top_sig$Signature <-lapply(top_sig$Signature,function(y){paste(y)})
top_sig$Cluster <-unique(unlist(top_sig$Cluster))
top_sig <- merge(y=top_sig, x=cluster_type[,c("Cluster","name_type")],by="Cluster")
colnames(top_sig)[2] <- "Assigned_Type"
kable(top_sig)
| 1 |
CD45 |
Macrophages |
832 |
5571 |
5.435 |
3.699 |
963 |
86.397 |
0.634 |
611 |
24.751 |
| 2 |
T_cells |
T_cells |
11147 |
103645 |
4.073 |
3.46 |
11716 |
95.143 |
0.658 |
7705 |
85.623 |
| 3 |
T_cells |
T_cells |
16150 |
139048 |
3.921 |
3.382 |
17068 |
94.622 |
0.602 |
10272.333 |
93.576 |
| 4 |
CD45 |
Neutrophils |
546 |
1239 |
1.998 |
2.304 |
1768 |
30.882 |
0.06 |
106.286 |
5.159 |
| 5 |
Macrophages |
Macrophages |
34 |
177 |
5.206 |
3.208 |
75 |
45.333 |
0.223 |
16.75 |
3.172 |
| 6 |
B_cells |
B_cells |
2187 |
21816 |
4.088 |
3.624 |
2282 |
95.837 |
0.507 |
1157.889 |
29.179 |
| 7 |
Cytotoxic_cells |
Cytotoxic_cells |
5882 |
283649 |
7.919 |
5.925 |
5900 |
99.695 |
3.563 |
21021.4 |
295.397 |
| 8 |
Cytotoxic_cells |
Cytotoxic_cells |
183 |
1727 |
7.256 |
4.298 |
202 |
90.594 |
0.521 |
105.3 |
10.058 |
| 9 |
Macrophages |
Macrophages |
10 |
16 |
1.6 |
1.897 |
25 |
40 |
0.11 |
2.75 |
0.901 |
| 10 |
Mast_cells |
Macrophages, Mast_cells |
1, 1 |
1, 9 |
1, 3 |
NA, 3.464 |
1, 1 |
100, 100 |
0.25, 1 |
0.25, 1 |
0.25, 1 |
cat("\n")
counter <-1
colnames(score_by_cluster) <- names(cell_list)
apply(score_by_cluster, 1,function(x) { plot_x <- plot(x,ylab="mean expression level per cell",xlab="cell type", main=c("Cluster",counter))
plot_x <- text(x, names(cell_list), cex=0.6, pos=4, col="red")
sum_table <- kable(all_type_expr_table[all_type_expr_table$Cluster == counter,])
plot_x
cat("\n")
print(sum_table)
cat("\n")
counter <<- counter + 1})

| 3 |
1 |
B_cells |
28 |
55 |
1.528 |
2.360 |
963 |
2.908 |
0.005 |
5 |
1.56 |
| 4 |
1 |
CD45 |
480 |
1681 |
3.502 |
3.304 |
963 |
49.844 |
0.811 |
781 |
42.485 |
| 5 |
1 |
CD8_T_cells |
39 |
114 |
2.651 |
2.869 |
963 |
4.050 |
0.031 |
29.5 |
5.545 |
| 6 |
1 |
Cytotoxic_cells |
303 |
1376 |
3.193 |
4.026 |
963 |
31.464 |
0.101 |
97.5 |
14.523 |
| 7 |
1 |
Exhausted_CD8 |
161 |
284 |
1.690 |
1.945 |
963 |
16.719 |
0.049 |
47.25 |
3.961 |
| 8 |
1 |
Macrophages |
832 |
5571 |
5.435 |
3.699 |
963 |
86.397 |
0.634 |
611 |
24.751 |
| 9 |
1 |
Neutrophils |
311 |
654 |
1.827 |
2.113 |
963 |
32.295 |
0.061 |
59.143 |
3.703 |
| 10 |
1 |
NK_CD56dim_cells |
21 |
21 |
1.000 |
0.000 |
963 |
2.181 |
0.005 |
5.25 |
1.146 |
| 11 |
1 |
NK_cells |
6 |
25 |
3.571 |
3.207 |
963 |
0.623 |
0.003 |
3.333 |
1.491 |
| 12 |
1 |
T_cells |
143 |
638 |
2.913 |
2.992 |
963 |
14.849 |
0.054 |
52.167 |
5.403 |
| 13 |
1 |
Th1_cells |
9 |
15 |
1.667 |
2.000 |
963 |
0.935 |
0.01 |
10 |
3.464 |
| 14 |
1 |
Treg |
2 |
2 |
1.000 |
0.000 |
963 |
0.208 |
0.002 |
2 |
1.414 |

| 15 |
2 |
B_cells |
340 |
795 |
2.049 |
2.444 |
11716 |
2.902 |
0.005 |
56.222 |
4.366 |
| 16 |
2 |
CD45 |
3646 |
9692 |
2.658 |
2.807 |
11716 |
31.120 |
0.42 |
4922 |
91.324 |
| 17 |
2 |
CD8_T_cells |
2649 |
11130 |
3.312 |
3.172 |
11716 |
22.610 |
0.222 |
2597.5 |
60.235 |
| 18 |
2 |
Cytotoxic_cells |
7866 |
112444 |
5.236 |
4.344 |
11716 |
67.139 |
0.529 |
6196.1 |
104.86 |
| 19 |
2 |
DC |
42 |
60 |
1.429 |
1.564 |
11716 |
0.358 |
0.001 |
15 |
2.38 |
| 20 |
2 |
Exhausted_CD8 |
1778 |
3240 |
1.724 |
1.991 |
11716 |
15.176 |
0.046 |
533.75 |
13.709 |
| 21 |
2 |
Macrophages |
282 |
408 |
1.442 |
1.613 |
11716 |
2.407 |
0.007 |
77 |
4.835 |
| 22 |
2 |
Mast_cells |
3 |
10 |
3.333 |
4.041 |
11716 |
0.026 |
0 |
1.25 |
0.829 |
| 23 |
2 |
Neutrophils |
19 |
25 |
1.316 |
1.376 |
11716 |
0.162 |
0 |
2.857 |
0.67 |
| 24 |
2 |
NK_CD56dim_cells |
173 |
268 |
1.540 |
1.779 |
11716 |
1.477 |
0.004 |
48.25 |
3.929 |
| 25 |
2 |
NK_cells |
402 |
1033 |
2.275 |
2.524 |
11716 |
3.431 |
0.016 |
189.333 |
10.934 |
| 26 |
2 |
T_cells |
11147 |
103645 |
4.073 |
3.460 |
11716 |
95.143 |
0.658 |
7705 |
85.623 |
| 27 |
2 |
Th1_cells |
305 |
408 |
1.338 |
1.393 |
11716 |
2.603 |
0.028 |
323 |
19 |
| 28 |
2 |
Treg |
84 |
163 |
1.940 |
2.214 |
11716 |
0.717 |
0.008 |
98 |
11.314 |

| 29 |
3 |
B_cells |
207 |
449 |
1.919 |
2.297 |
17068 |
1.213 |
0.002 |
32.444 |
2.927 |
| 30 |
3 |
CD45 |
4863 |
11961 |
2.460 |
2.661 |
17068 |
28.492 |
0.368 |
6286 |
99.499 |
| 31 |
3 |
CD8_T_cells |
4141 |
21377 |
3.927 |
3.352 |
17068 |
24.262 |
0.274 |
4681 |
85.15 |
| 32 |
3 |
Cytotoxic_cells |
5187 |
13357 |
2.174 |
2.567 |
17068 |
30.390 |
0.046 |
791.2 |
15.642 |
| 33 |
3 |
DC |
8 |
8 |
1.000 |
0.000 |
17068 |
0.047 |
0 |
2.667 |
0.943 |
| 34 |
3 |
Exhausted_CD8 |
1001 |
1495 |
1.477 |
1.644 |
17068 |
5.865 |
0.016 |
275 |
9.083 |
| 35 |
3 |
Macrophages |
248 |
321 |
1.294 |
1.309 |
17068 |
1.453 |
0.004 |
65.25 |
4.25 |
| 36 |
3 |
Mast_cells |
4 |
16 |
4.000 |
3.464 |
17068 |
0.023 |
0 |
1.5 |
0.791 |
| 37 |
3 |
Neutrophils |
31 |
38 |
1.188 |
1.061 |
17068 |
0.182 |
0 |
4.714 |
0.869 |
| 38 |
3 |
NK_CD56dim_cells |
137 |
173 |
1.263 |
1.232 |
17068 |
0.803 |
0.002 |
35.75 |
3.112 |
| 39 |
3 |
NK_cells |
28 |
51 |
1.594 |
1.881 |
17068 |
0.164 |
0.001 |
12 |
2.494 |
| 40 |
3 |
T_cells |
16150 |
139048 |
3.921 |
3.382 |
17068 |
94.622 |
0.602 |
10272.333 |
93.576 |
| 41 |
3 |
Th1_cells |
64 |
82 |
1.281 |
1.278 |
17068 |
0.375 |
0.004 |
67 |
8.544 |
| 42 |
3 |
Treg |
30 |
55 |
1.833 |
2.167 |
17068 |
0.176 |
0.002 |
35 |
6.856 |

| 43 |
4 |
B_cells |
58 |
149 |
2.328 |
2.679 |
1768 |
3.281 |
0.005 |
9.333 |
1.457 |
| 44 |
4 |
CD45 |
265 |
585 |
2.208 |
2.528 |
1768 |
14.989 |
0.189 |
335 |
23 |
| 45 |
4 |
CD8_T_cells |
41 |
94 |
2.136 |
2.446 |
1768 |
2.319 |
0.015 |
27 |
5 |
| 46 |
4 |
Cytotoxic_cells |
387 |
1881 |
3.329 |
3.853 |
1768 |
21.889 |
0.072 |
126.6 |
12.272 |
| 47 |
4 |
DC |
1 |
1 |
1.000 |
NA |
1768 |
0.057 |
0 |
0.333 |
0.333 |
| 48 |
4 |
Exhausted_CD8 |
99 |
151 |
1.480 |
1.657 |
1768 |
5.600 |
0.016 |
27.75 |
2.926 |
| 49 |
4 |
Macrophages |
391 |
769 |
1.835 |
2.167 |
1768 |
22.115 |
0.07 |
123.5 |
6.973 |
| 50 |
4 |
Neutrophils |
546 |
1239 |
1.998 |
2.304 |
1768 |
30.882 |
0.06 |
106.286 |
5.159 |
| 51 |
4 |
NK_CD56dim_cells |
7 |
19 |
2.714 |
2.928 |
1768 |
0.396 |
0.001 |
2.25 |
0.901 |
| 52 |
4 |
NK_cells |
9 |
11 |
1.000 |
0.000 |
1768 |
0.509 |
0.002 |
3.667 |
1.291 |
| 53 |
4 |
T_cells |
259 |
719 |
2.153 |
2.488 |
1768 |
14.649 |
0.039 |
69.833 |
5.398 |
| 54 |
4 |
Th1_cells |
8 |
8 |
1.000 |
0.000 |
1768 |
0.452 |
0.005 |
8 |
2.828 |

| 55 |
5 |
CD45 |
2 |
2 |
1.000 |
0.000 |
75 |
2.667 |
0.027 |
2 |
1.414 |
| 56 |
5 |
CD8_T_cells |
1 |
7 |
7.000 |
NA |
75 |
1.333 |
0.013 |
1 |
1 |
| 57 |
5 |
Cytotoxic_cells |
21 |
147 |
3.769 |
4.837 |
75 |
28.000 |
0.192 |
14.4 |
6.81 |
| 58 |
5 |
Macrophages |
34 |
177 |
5.206 |
3.208 |
75 |
45.333 |
0.223 |
16.75 |
3.172 |
| 59 |
5 |
NK_cells |
1 |
1 |
1.000 |
NA |
75 |
1.333 |
0.004 |
0.333 |
0.333 |
| 60 |
5 |
T_cells |
6 |
35 |
3.182 |
3.027 |
75 |
8.000 |
0.033 |
2.5 |
1.213 |
| 61 |
5 |
Th1_cells |
1 |
1 |
1.000 |
NA |
75 |
1.333 |
0.013 |
1 |
1 |

| 62 |
6 |
B_cells |
2187 |
21816 |
4.088 |
3.624 |
2282 |
95.837 |
0.507 |
1157.889 |
29.179 |
| 63 |
6 |
CD45 |
539 |
1249 |
2.317 |
2.581 |
2282 |
23.620 |
0.3 |
684 |
32.741 |
| 64 |
6 |
CD8_T_cells |
59 |
149 |
2.191 |
2.639 |
2282 |
2.585 |
0.02 |
44.5 |
7.194 |
| 65 |
6 |
Cytotoxic_cells |
377 |
2065 |
3.542 |
4.474 |
2282 |
16.521 |
0.063 |
143.7 |
18.319 |
| 66 |
6 |
Exhausted_CD8 |
59 |
77 |
1.305 |
1.329 |
2282 |
2.585 |
0.007 |
15.5 |
2.062 |
| 67 |
6 |
Macrophages |
82 |
116 |
1.398 |
1.592 |
2282 |
3.593 |
0.01 |
22.75 |
2.704 |
| 68 |
6 |
Mast_cells |
1 |
1 |
1.000 |
NA |
2282 |
0.044 |
0 |
0.25 |
0.25 |
| 69 |
6 |
Neutrophils |
20 |
20 |
1.000 |
0.000 |
2282 |
0.876 |
0.001 |
2.857 |
0.639 |
| 70 |
6 |
NK_CD56dim_cells |
20 |
20 |
1.000 |
0.000 |
2282 |
0.876 |
0.002 |
5 |
1.118 |
| 71 |
6 |
NK_cells |
5 |
5 |
1.000 |
0.000 |
2282 |
0.219 |
0.001 |
1.667 |
0.745 |
| 72 |
6 |
T_cells |
306 |
1375 |
2.847 |
3.011 |
2282 |
13.409 |
0.051 |
116.667 |
8.715 |
| 73 |
6 |
Th1_cells |
16 |
16 |
1.000 |
0.000 |
2282 |
0.701 |
0.007 |
16 |
4 |
| 74 |
6 |
Treg |
1 |
1 |
1.000 |
NA |
2282 |
0.044 |
0 |
1 |
1 |

| 75 |
7 |
B_cells |
74 |
270 |
2.477 |
3.066 |
5900 |
1.254 |
0.003 |
20.111 |
3.7 |
| 76 |
7 |
CD45 |
2104 |
6099 |
2.899 |
2.948 |
5900 |
35.661 |
0.503 |
2969 |
73.451 |
| 77 |
7 |
CD8_T_cells |
2505 |
10733 |
3.266 |
3.113 |
5900 |
42.458 |
0.421 |
2483 |
58.292 |
| 78 |
7 |
Cytotoxic_cells |
5882 |
283649 |
7.919 |
5.925 |
5900 |
99.695 |
3.563 |
21021.4 |
295.397 |
| 79 |
7 |
DC |
1 |
1 |
1.000 |
NA |
5900 |
0.017 |
0 |
0.333 |
0.333 |
| 80 |
7 |
Exhausted_CD8 |
996 |
1769 |
1.663 |
1.924 |
5900 |
16.881 |
0.051 |
299.75 |
10.359 |
| 81 |
7 |
Macrophages |
92 |
151 |
1.641 |
2.020 |
5900 |
1.559 |
0.004 |
26.5 |
3.202 |
| 82 |
7 |
Neutrophils |
12 |
12 |
1.000 |
0.000 |
5900 |
0.203 |
0 |
1.714 |
0.495 |
| 83 |
7 |
NK_CD56dim_cells |
414 |
713 |
1.647 |
1.908 |
5900 |
7.017 |
0.021 |
122 |
6.461 |
| 84 |
7 |
NK_cells |
1052 |
2835 |
2.305 |
2.589 |
5900 |
17.831 |
0.089 |
523.333 |
19.206 |
| 85 |
7 |
T_cells |
3853 |
33071 |
4.142 |
3.510 |
5900 |
65.305 |
0.42 |
2477.167 |
47.877 |
| 86 |
7 |
Th1_cells |
848 |
1558 |
1.837 |
2.108 |
5900 |
14.373 |
0.166 |
978 |
35.609 |
| 87 |
7 |
Treg |
7 |
7 |
1.000 |
0.000 |
5900 |
0.119 |
0.001 |
7 |
2.646 |

| 88 |
8 |
B_cells |
132 |
635 |
3.489 |
3.304 |
202 |
65.347 |
0.162 |
32.778 |
3.561 |
| 89 |
8 |
CD45 |
16 |
29 |
1.812 |
2.228 |
202 |
7.921 |
0.094 |
19 |
5.196 |
| 90 |
8 |
CD8_T_cells |
6 |
18 |
3.000 |
3.098 |
202 |
2.970 |
0.02 |
4 |
1.732 |
| 91 |
8 |
Cytotoxic_cells |
183 |
1727 |
7.256 |
4.298 |
202 |
90.594 |
0.521 |
105.3 |
10.058 |
| 92 |
8 |
Exhausted_CD8 |
3 |
3 |
1.000 |
0.000 |
202 |
1.485 |
0.004 |
0.75 |
0.433 |
| 93 |
8 |
Macrophages |
59 |
170 |
2.576 |
2.701 |
202 |
29.208 |
0.105 |
21.25 |
3.072 |
| 94 |
8 |
Neutrophils |
8 |
8 |
1.000 |
0.000 |
202 |
3.960 |
0.006 |
1.143 |
0.404 |
| 95 |
8 |
NK_CD56dim_cells |
1 |
1 |
1.000 |
NA |
202 |
0.495 |
0.001 |
0.25 |
0.25 |
| 96 |
8 |
NK_cells |
1 |
1 |
1.000 |
NA |
202 |
0.495 |
0.002 |
0.333 |
0.333 |
| 97 |
8 |
T_cells |
35 |
176 |
3.592 |
3.175 |
202 |
17.327 |
0.063 |
12.667 |
2.539 |
| 98 |
8 |
Th1_cells |
2 |
2 |
1.000 |
0.000 |
202 |
0.990 |
0.01 |
2 |
1.414 |

| 99 |
9 |
B_cells |
1 |
1 |
1.0 |
NA |
25 |
4 |
0.004 |
0.111 |
0.111 |
| 100 |
9 |
Cytotoxic_cells |
4 |
4 |
1.0 |
0.000 |
25 |
16 |
0.016 |
0.4 |
0.2 |
| 101 |
9 |
Macrophages |
10 |
16 |
1.6 |
1.897 |
25 |
40 |
0.11 |
2.75 |
0.901 |
| 102 |
9 |
T_cells |
2 |
2 |
1.0 |
0.000 |
25 |
8 |
0.013 |
0.333 |
0.236 |

| 10 |
Macrophages |
1 |
1 |
1 |
NA |
1 |
100 |
0.25 |
0.25 |
0.25 |
| 10 |
Mast_cells |
1 |
9 |
3 |
3.464 |
1 |
100 |
1 |
1 |
1 |
[1] 2 3 4 5 6 7 8 9 10 11
for( i in 1:length(mean_score[1,])){
print(visualize_me(mean_score[,i],cell_list[i],analysis_results$tsne[c("TSNE.1","TSNE.2")],title=names(cell_list)[i]))
#print(plot(mean_score[,i],type = "h",xlab="Single Cell",ylab=colnames(mean_score)[i]))
h <-hist(mean_score[,i],plot = FALSE)
h<- plot(h, freq = TRUE, labels =TRUE, ylim=c(0, 1.2*max(h$counts)),main=c(names(cell_list)[i]," Score per Single Cell"),xlab=paste(sep=" ",names(cell_list)[i],"Expression Level"),ylab="Numbers of cells")
#lay_out(list(h, 1, 1),
# list(vm, 1, 2))
}



























